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caper (version 0.4)

Comparative Analyses of Phylogenetics and Evolution in R

Description

Functions for performing phylogenetic comparative analyses.

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Version

Install

install.packages('caper')

Monthly Downloads

3,376

Version

0.4

License

GPL (>= 2)

Maintainer

David Orme

Last Published

June 3rd, 2011

Functions in caper (0.4)

IsaacEtAl

Example dataset for the caper package

crunch

Comparative analysis using the crunch algorithm.

pgls

Phylogenetic generalized linear models

anova.pgls

Anova and AIC tables for 'pgls' models.

clade.matrix

Create a clade matrix from a phylogeny

fuscoData

Example dataset for Fusco imbalance calculations

pgls-methods

Generic model methods for 'pgls' models.

BritishBirds

Conservation status of British birds (Thomas 2008)

plot.pgls

Diagnostic plots for 'pgls' models.

phylo.d

Calculates the phylogenetic D statistic

clade.members

Identify tips descended from a node

caper-benchmarks

Datasets used for benchmarking caper

syrphidae

The syrphidae dataset of Katzourakis et al. 2001

caper-package

Comparative analysis of phylogenetics and evolution in R (caper)

pd.calc

Calculate and bootstrap phylogenetic diversity measurements.

summary.caic

Summarize a crunch, brunch or macrocaic analysis

fusco.test

Imbalance statistics using Fusco and Cronk's method.

perissodactyla

Example dataset for the CAIC package

comparative.data

Comparative dataset creation

anova.caic

Anova and model checking methods for independent contrast models.

brunch

Comparative analysis using the brunch algorithm.

macrocaic

Comparative analysis using independent contrasts on species richness data.

caic-class

The 'caic' S3 object class and methods

pgls.profile

Likelihood profiles and confidence intervals for 'pgls' models.

growTree

Tree simulation with traits.

VCV.array

Create a 2D or 3D variance-covariance matrix from a phylogeny

caic.diagnostics

Diagnostic tools for independent contrasts models

shorebird

Example dataset for the caper package